def testToOpenMSFeatureMap():
t = Table("mz rt".split(), [float, float], 2 * ["%.6f"])
fm = toOpenMSFeatureMap(t)
assert fm.size() == 0
t.addRow([1.0, 2.0])
fm = toOpenMSFeatureMap(t)
assert fm.size() == 1
f = fm[0]
assert f.getMZ() == 1.0 # == ok, as no digits after decimal point
assert f.getRT() == 2.0 # dito
def isotopeDistributionTable(formula, R=None, fullC13=False, minp=0.01, **kw):
"""
generates Table for most common isotopes of molecule with given mass
*formula*.
If the resolution *R* is given, the measurement device is simulated, and
overlapping peaks may merge.
*fullC13=True* assumes that only C13 carbon is present in formula.
Further you can give a threshold *minp* for considering only isotope
peaks with an abundance above the value. Standard is *minp=0.01*.
If you have special elementary isotope abundances which differ from
the natural abundances, you can tell that like
``ms.isotopeDistributionTable("S4C4", C=dict(C13=0.5, C12=0.5))``
Examples:
.. pycon::
import ms !onlyoutput
# natural abundances:
tab = ms.isotopeDistributionTable("C3H7NO2")
tab.abundance /= tab.abundance.sum()
tab.print_()
# artifical abundances:
tab = ms.isotopeDistributionTable("C3H7NO2", C=dict(C13=0.5, C12=0.5))
tab.abundance /= tab.abundance.sum()
tab.print_()
\
"""
from libms.DataStructures.Table import Table
gen = _setupIsotopeDistributionGenerator(formula, R, fullC13, minp, **kw)
t = Table(["mf", "mass", "abundance"], [str, float, float],
["%s", "%.6f", "%.3f"], [])
for mass, abundance in gen.getCentroids():
t.addRow([formula, mass, abundance], False)
t.resetInternals()
return t
def isotopeDistributionTable(formula, R=None, fullC13=False, minp=0.01, **kw):
"""
generates Table for most common isotopes of molecule with given mass
*formula*.
If the resolution *R* is given, the measurement device is simulated, and
overlapping peaks may merge.
*fullC13=True* assumes that only C13 carbon is present in formula.
Further you can give a threshold *minp* for considering only isotope
peaks with an abundance above the value. Standard is *minp=0.01*.
If you have special elementary isotope abundances which differ from
the natural abundances, you can tell that like
``ms.isotopeDistributionTable("S4C4", C=dict(C13=0.5, C12=0.5))``
Examples:
.. pycon::
import ms !onlyoutput
# natural abundances:
tab = ms.isotopeDistributionTable("C3H7NO2")
tab.abundance /= tab.abundance.sum()
tab.print_()
# artifical abundances:
tab = ms.isotopeDistributionTable("C3H7NO2", C=dict(C13=0.5, C12=0.5))
tab.abundance /= tab.abundance.sum()
tab.print_()
\
"""
from libms.DataStructures.Table import Table
gen = _setupIsotopeDistributionGenerator(formula, R, fullC13, minp, **kw)
t = Table(["mf", "mass", "abundance"], [str, float, float],
["%s", "%.6f", "%.3f"], [])
for mass, abundance in gen.getCentroids():
t.addRow([formula, mass, abundance], False)
t.resetInternals()
return t